Theoretical study of absorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) on TiO₂(110) rutile surface.

abstract：:Prion diseases are associated with misfolding and aggregation of prion protein (PrP). Cellular prion protein contains a disulfide bond linking Cys residues at positions 179 and 214. It has been proposed that this disulfide bond plays an important role in the conversion between cellular (PrP(C)) and the scrapie form of...

journal_title：Journal of molecular modeling

authors： Ning L,Guo J,Jin N,Liu H,Yao X

更新日期：2014-02-01 00:00:00

abstract：:The ion-pair S(N)2 reaction LiNCS + CH3F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction p...

journal_title：Journal of molecular modeling

authors： Ren Y,Li M,Wong NB,Chu SY

更新日期：2006-01-01 00:00:00

abstract：:The incidence of tuberculosis infections that are resistant to conventional drug therapy has risen steadily in the last decade. Several of the quinolone antibacterials have been examined as inhibitors of M. tuberculosis infection as well as other mycobacterial infections. However, not much has been done to examine spe...

journal_title：Journal of molecular modeling

authors： Bagchi MC,Mills D,Basak SC

更新日期：2007-01-01 00:00:00

abstract：:The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The...

journal_title：Journal of molecular modeling

authors： Czeleń P,Cysewski P

更新日期：2013-08-01 00:00:00

abstract：:It is well-established that many covalently-bonded atoms of Groups IV-VII have directionally-specific regions of positive electrostatic potential (σ-holes) through which they can interact with negative sites. In the case of Group VII, this is called "halogen bonding." We have studied two series of molecules: the F3MX ...

journal_title：Journal of molecular modeling

authors： Bundhun A,Ramasami P,Murray JS,Politzer P

更新日期：2013-07-01 00:00:00

abstract：:We design four high performance non-fullerene acceptor materials by applying strong electron withdrawing groups at the end of A-D-A-D-A type organic solar cells molecules and compute their different opto-electronic and photovoltaic properties, including absorption spectrum, electron density, solubility strength, charg...

journal_title：Journal of molecular modeling

authors： Ali U,Javed A,Tallat A,Iqbal J,Raza A

更新日期：2019-01-31 00:00:00

abstract：:Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

journal_title：Journal of molecular modeling

authors： Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

更新日期：2011-10-01 00:00:00

abstract：:The geometrical, conformational, and electronic properties of a series of D-π-A metal-free dyes designed for use as sensitizers in DSSCs were studied using DFT and TD-DFT methods. A substituted triphenylamine moiety was used as the donor group and 2-cyanoacrylic acid as the acceptor group in these dyes. They also cont...

journal_title：Journal of molecular modeling

authors： Hasanein AA,Elmarassi YR,Kassem EN

更新日期：2016-05-01 00:00:00

abstract：:Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined. ...

journal_title：Journal of molecular modeling

authors： Wedler HB,Pemberton RP,Lounnas V,Vriend G,Tantillo DJ,Wang SC

更新日期：2015-05-01 00:00:00

abstract：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...

journal_title：Journal of molecular modeling

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00

abstract：:Using molecular dynamics simulations, we investigated the thermal stability and real-time denaturation of a model mini-protein in four solvents: (1) water, (2) 1-ethyl-3-methylimidazolium alaninate [EMIM][ALA] (5 mol% in water), (3) methioninate [EMIM][MET] (5 mol% in water), and (4) tryptophanate [EMIM][TRP] (5 mol% ...

journal_title：Journal of molecular modeling

authors： Chevrot G,Fileti EE,Chaban VV

更新日期：2016-11-01 00:00:00

abstract：:The aqueous solvation of Th and Np in the IV oxidation state was examined using cluster models generated by Monte Carlo simulations and density functional theory embedded within the COSMO continuum model to approximate the effect of bulk water. Our results suggest that the coordination number (CN) for both Th(IV) and ...

journal_title：Journal of molecular modeling

authors： Amador DH,Sambrano JR,Gargano R,de Macedo LG

更新日期：2017-03-01 00:00:00

abstract：:Colorectal cancer, which is considered one of the leading causes of mortality worldwide, develops through the formation of benign polyps on the inner colon or rectum wall. Truncations in adenomatous polyposis coli (APC) gene lead to the spread of the disease in the entire colon region when combined with the guanine nu...

journal_title：Journal of molecular modeling

authors： Jadav SS,Macalino SJY,Alluri R

更新日期：2020-07-16 00:00:00

abstract：:Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein seque...

journal_title：Journal of molecular modeling

authors： Saraswathi S,Fernández-Martínez JL,Kolinski A,Jernigan RL,Kloczkowski A

更新日期：2012-09-01 00:00:00

abstract：:Numerous studies suggest that two-phase morphology and thick interface are separately beneficial to the viscosity reduction and mechanical property maintainence of the matrix when normal molecular weight polymer (NMWP) is used for modification of ultrahigh molecular weight polyethylene (UHMWPE). Nevertheless, it is ve...

journal_title：Journal of molecular modeling

authors： Gai JG,Zuo Y

更新日期：2012-06-01 00:00:00

abstract：:The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Densi...

journal_title：Journal of molecular modeling

authors： Toczek D,Kubas K,Turek M,Roszak S,Gancarz R

更新日期：2013-10-01 00:00:00

abstract：:Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...

journal_title：Journal of molecular modeling

authors： Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MA

更新日期：2015-05-01 00:00:00

abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...

journal_title：Journal of molecular modeling

authors： Mitra P,Pal D

更新日期：2011-03-01 00:00:00

abstract：:In the present study, DFT calculations are carried out on domestically designed 7-methyl-2-phenyl-5'H-spiro[chromene-4,2'-chromeno[3,4-e][1,3]oxazin]-5'-one spiropyran and merocyanine derivatives to recognize alkali and alkaline earth metal ions. Detection of these metal ions can be attained by exploiting the variatio...

journal_title：Journal of molecular modeling

authors： Arif AM,Yousaf A,Zhong RL,Akhtar M,Muhammad S,Xu HL,Su ZM

更新日期：2019-07-06 00:00:00

abstract：:The aim of this study was to perform an in silico analysis of the interaction of the human beta(2) adrenergic receptor with Galpha(s). In a first step, a systematic surface-interaction-scan between the inactive or active human beta(2) adrenergic receptor and Galpha(s) was performed in order to gain knowledge about ene...

journal_title：Journal of molecular modeling

authors： Strasser A,Wittmann HJ

更新日期：2010-08-01 00:00:00

abstract：:The heats of formation (HOFs), electronic structure, energetic properties, and thermal stabilities for a series of 1,4-bis(1-azo-2,4-dinitrobenzene)-iminotetrazole derivatives with different substituents and substitution positions and numbers of nitrogen atoms in the nitrobenzene rings were studied using the DFT-B3LYP...

journal_title：Journal of molecular modeling

authors： Wu Q,Pan Y,Zhu W,Xiao H

更新日期：2013-04-01 00:00:00

abstract：:The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain p...

journal_title：Journal of molecular modeling

authors： Ahmad F,Shabaz Z,Azam SS

更新日期：2020-08-03 00:00:00

abstract：:The preferential selectivity of dicyclohexano-18-crown-6 (DCH18C6) for bivalent Sr(+2) ion over tetravalent Th(+4) ion was investigated using generalized gradient approximated (GGA) BP86 and the hybrid B3LYP density functional, employing split valence plus polarization (SV(P)) and triple-zeta valence plus polarization...

journal_title：Journal of molecular modeling

authors： Boda A,Joshi JM,Ali SM,Shenoy KT,Ghosh SK

更新日期：2013-12-01 00:00:00

abstract：:The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05-2X theories using the 6-31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a conce...

journal_title：Journal of molecular modeling

authors： Yildiz CB,Azizoglu A

更新日期：2016-07-01 00:00:00

abstract：:Nowadays, scientists are trying to develop low-cost fullerene free acceptors for small organic photovoltaic cells in order to overcome the limitations of fullerene derivatives. Current research work deals with theoretical study on three non-fullerene acceptors based on indaceno, dithiophene core, and thiophene bridge ...

journal_title：Journal of molecular modeling

authors： Ajmal M,Ali U,Javed A,Tariq A,Arif Z,Iqbal J,Shoaib M,Ahmed T

更新日期：2019-09-11 00:00:00

abstract：:The aquatic leech, Theromyzon tessulatum, secretes a proteinaceous cocoon with extraordinary physical properties (e.g., proteolytic, thermal resiliency). The deduced amino acid sequence of a major protein (Tcp-Theromyzon cocoon protein) from the T. tessulatum cocoon wall has been used to model the endogenous structure...

journal_title：Journal of molecular modeling

authors： Mason TA,McIlroy PJ,Shain DH

更新日期：2006-09-01 00:00:00

abstract：:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very ...

journal_title：Journal of molecular modeling

authors： Riley KE,Murray JS,Fanfrlík J,Rezáč J,Solá RJ,Concha MC,Ramos FM,Politzer P

更新日期：2011-12-01 00:00:00

abstract：:In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic...

journal_title：Journal of molecular modeling

authors： Rosli AN,Abu Bakar MA,Lee VS,Zain SM,Ahmad MR,Abdul Manan NS,Alias Y,Woi PM

更新日期：2014-09-01 00:00:00

abstract：:Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C-H(…)π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals t...

journal_title：Journal of molecular modeling

authors： Dinadayalane TC,Paytakov G,Leszczynski J

更新日期：2013-07-01 00:00:00

abstract：:Structure-olfactive threshold relationships for 40 pyrazine derivatives have been studied by multivariate statistical analysis. Variable descriptors used to describe the molecules studied were obtained using molecular-mechanics software. A correlation coefficient of 0.82 was obtained when all the molecules were includ...

journal_title：Journal of molecular modeling

authors： Zakarya D,Farhaoui L,Hamidi M,Bouachrine M

更新日期：2006-09-01 00:00:00